A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

@article{Alioto2015ACA,
  title={A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.},
  author={Tyler S Alioto and Ivo Buchhalter and Sophia Derdak and Barbara Hutter and Matthew Eldridge and Eivind Hovig and Lawrence E. Heisler and Timothy A Beck and Jared T. Simpson and Laurie Tonon and Anne-Sophie Sertier and Ann-Marie Patch and Natalie J{\"a}ger and Philip Ginsbach and Ruben Drews and Nagarajan Paramasivam and Rolf Kabbe and Sasithorn Chotewutmontri and Nicolle Diessl and Christopher Previti and Sabine S. Schmidt and Benedikt Brors and Lars Feuerbach and Michael Heinold and Susanne N. Gr{\"o}bner and Andrey Korshunov and Patrick S. Tarpey and Adam P. Butler and Jonathan W. Hinton and David Jones and Andrew Menzies and Keiran M Raine and Rebecca Shepherd and Lucy A. Stebbings and Jon W. Teague and Paolo Ribeca and Francesc Castro Giner and Sergi Beltr{\'a}n and Emanuele Raineri and Marc Dabad and Simon C Heath and Marta Gut and Robert E Denroche and Nicholas J. Harding and Takafumi N. Yamaguchi and Akihiro Fujimoto and Hidewaki Nakagawa and V{\'i}ctor Quesada and Rafael Vald{\'e}s-Mas and Sigve Nakken and Daniel Vod{\'a}k and Lawrence Bower and Andrew G Lynch and Charlotte Anderson and Nicola Waddell and John V. Pearson and Sean M. Grimmond and Myron Peto and Paul T. Spellman and Minghui He and Cyriac Kandoth and Semin Lee and John H Zhang and Louis L{\'e}tourneau and Singer Ma and Sahil Seth and David Torrents and Liu Xi and David A. Wheeler and Carlos L{\'o}pez-Ot{\'i}n and El{\'i}as Campo and Peter J. Campbell and Paul C. Boutros and Xose S. Puente and Daniela S. Gerhard and Stefan M. Pfister and John D. McPherson and Thomas J. Hudson and Matthias Schlesner and Peter Lichter and Roland Eils and D T W Jones and Ivo G Gut},
  journal={Nature communications},
  year={2015},
  volume={6},
  pages={10001}
}
As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free… CONTINUE READING
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